BioC 3.6: CHECK report for GOexpress on malbec1

Package: GOexpress

Version: 1.11.0

Command: /home/biocbuild/bbs-3.6-bioc/R/bin/R CMD check --no-vignettes --timings GOexpress_1.11.0.tar.gz

StartedAt: 2017-08-15 23:38:48 -0400 (Tue, 15 Aug 2017)

EndedAt: 2017-08-15 23:40:26 -0400 (Tue, 15 Aug 2017)

EllapsedTime: 98.2 seconds

RetCode: 0

Status:  OK

CheckDir: GOexpress.Rcheck

Warnings: 0

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### Running command:
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###   /home/biocbuild/bbs-3.6-bioc/R/bin/R CMD check --no-vignettes --timings GOexpress_1.11.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.6-bioc/meat/GOexpress.Rcheck’
* using R version 3.4.1 (2017-06-30)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘GOexpress/DESCRIPTION’ ... OK
* this is package ‘GOexpress’ version ‘1.11.0’
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘GOexpress’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking loading without being on the library search path ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
GO_analyse: no visible binding for global variable ‘microarray2dataset’
GO_analyse: no visible binding for global variable ‘prefix2dataset’
mart_from_ensembl: no visible binding for global variable
  ‘prefix2dataset’
Undefined global functions or variables:
  microarray2dataset prefix2dataset
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 1 NOTE
See
  ‘/home/biocbuild/bbs-3.6-bioc/meat/GOexpress.Rcheck/00check.log’
for details.

* installing *source* package ‘GOexpress’ ...
** R
** data
*** moving datasets to lazyload DB
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (GOexpress)

name	user	system	elapsed
AlvMac	0.128	0.004	0.129
AlvMac_GOgenes	0.424	0.040	0.463
AlvMac_allGO	0.020	0.000	0.022
AlvMac_allgenes	0.012	0.000	0.013
AlvMac_results	0.296	0.056	0.351
AlvMac_results.pVal	2.828	0.356	3.187
GO_analyse	2.644	0.052	2.698
GOexpress-package	0.000	0.000	0.003
cluster_GO	0.144	0.000	0.143
expression_plot	2.904	0.000	2.902
expression_plot_symbol	1.016	0.012	1.028
expression_profiles	0.648	0.000	0.650
expression_profiles_symbol	0.896	0.000	0.892
heatmap_GO	1.188	0.024	1.219
hist_scores	0.220	0.000	0.218
list_genes	0.100	0.016	0.117
microarray2dataset	0.008	0.000	0.009
pValue_GO	0	0	0
plot_design	0.152	0.000	0.153
prefix2dataset	0.008	0.000	0.010
quantiles_scores	0.208	0.016	0.224
rerank	0.236	0.016	0.249
subEset	0.044	0.004	0.048
subset_scores	0.392	0.024	0.416
table_genes	0.108	0.004	0.111